; oligo-analysis -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Danio_rerio_EnsEMBL/genome/Danio_rerio_EnsEMBL_start_codons.wc -o $RSAT/public_html/data/genomes/Danio_rerio_EnsEMBL/genome/Danio_rerio_EnsEMBL_start_codon_frequencies.tab ; Citation: van Helden et al. (1998). J Mol Biol 281(5), 827-42. ; Program version 1.169 ; Slow counting mode ; Oligomer length 3 ; Input file $RSAT/public_html/data/genomes/Danio_rerio_EnsEMBL/genome/Danio_rerio_EnsEMBL_start_codons.wc ; Input format wc ; Output file $RSAT/public_html/data/genomes/Danio_rerio_EnsEMBL/genome/Danio_rerio_EnsEMBL_start_codon_frequencies.tab ; Count overlapping matches ; Counted on a single strand ; Background model Bernoulli ; Background estimation method ; Sequence type DNA ; Nb of sequences 29304 ; Sum of sequence lengths 87912 ; discarded residues 32 (other letters than ACGT) ; discarded occurrences 21 (contain discarded residues) ; nb possible positions 29283 ; total oligo occurrences 29283 ; alphabet size 4 ; nb possible oligomers 64 ; oligomers tested for significance 0 ; ; column headers ; 1 seq oligomer sequence ; 2 id oligomer identifier ; 3 obs_freq observed relative frequency ; 4 occ observed occurrences #seq id obs_freq occ atg atg 0.5549294812690 16250 cag cag 0.0194310692210 569 ctg ctg 0.0156063244886 457 gtg gtg 0.0148208858382 434 ttt ttt 0.0141378957074 414 gag gag 0.0127719154458 374 att att 0.0122255233412 358 aaa aaa 0.0117132807431 343 ttg ttg 0.0109278420927 320 gtt gtt 0.0104497490011 306 ctt ctt 0.0101765529488 298 tgt tgt 0.0099716559096 292 ctc ctc 0.0098692073900 289 gaa gaa 0.0098350578834 288 atc atc 0.0095618618311 280 gat gat 0.0094935628180 278 tca tca 0.0094594133115 277 aag aag 0.0093569647919 274 tta tta 0.0091862172592 269 tct tct 0.0091520677526 268 agg agg 0.0087081241676 255 agt agt 0.0087081241676 255 gac gac 0.0086739746611 254 aca aca 0.0085715261414 251 ata ata 0.0084007786087 246 gga gga 0.0082983300891 243 aga aga 0.0080934330499 237 ttc ttc 0.0079226855172 232 caa caa 0.0078885360107 231 agc agc 0.0074787419322 219 gca gca 0.0072738448929 213 aat aat 0.0072055458799 211 ggt ggt 0.0068640508145 201 gct gct 0.0066591537752 195 tat tat 0.0065567052556 192 tcc tcc 0.0063176587098 185 tgc tgc 0.0063176587098 185 gtc gtc 0.0062493596968 183 cca cca 0.0061469111771 180 aac aac 0.0059761636444 175 gta gta 0.0058737151248 172 cta cta 0.0053614725267 157 tac tac 0.0052931735136 155 cct cct 0.0050882764744 149 cac cac 0.0049858279548 146 tgg tgg 0.0045418843698 133 act act 0.0044052863436 129 gcc gcc 0.0043369873305 127 cat cat 0.0040296417717 118 acc acc 0.0039613427586 116 ggc ggc 0.0038930437455 114 ccg ccg 0.0034832496670 102 gcg gcg 0.0034149506540 100 ggg ggg 0.0033466516409 98 ccc ccc 0.0031076050951 91 tcg tcg 0.0030734555886 90 acg acg 0.0026295120036 77 cgt cgt 0.0022197179251 65 cgc cgc 0.0021514189120 63 cgg cgg 0.0017416248335 51 cga cga 0.0016733258204 49 ; Host name n55 ; Job started 2017-04-15.090030 ; Job done 2017-04-15.090031 ; Seconds 0.4 ; user 0.4 ; system 0.03 ; cuser 0 ; csystem 0